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In [[quantitative genetics]], '''Q<sub>ST</sub>''' is a statistic intended to measure the degree of [[Genetic distance|genetic differentiation]] among populations with regard to a [[quantitative trait]]. It was developed by Ken Spitze in 1993.<ref name="Spitze_1993">{{cite journal | vauthors = Spitze K | title = Population structure in Daphnia obtusa: quantitative genetic and allozymic variation | journal = Genetics | volume = 135 | issue = 2 | pages = 367–374 | date = October 1993 | pmid = 8244001 | pmc = 1205642 | doi = 10.1093/genetics/135.2.367 }}</ref> Its name reflects that Q<sub>ST</sub> was intended to be analogous to the [[fixation index]] for a single [[genetic locus]] (F<sub>ST</sub>).<ref>{{cite journal | vauthors = Whitlock MC | title = Evolutionary inference from QST | journal = Molecular Ecology | volume = 17 | issue = 8 | pages = 1885–1896 | date = April 2008 | pmid = 18363667 | doi = 10.1111/j.1365-294X.2008.03712.x | doi-access = free }}</ref><ref>{{Cite journal | vauthors = McKay JK, Latta RG |date=June 2002 |title=Adaptive population divergence: markers, QTL and traits |journal=[[Trends in Ecology & Evolution]] |language=en |volume=17 |issue=6 |pages=285–291 |doi=10.1016/S0169-5347(02)02478-3}}</ref> Q<sub>ST</sub> is often compared with F<sub>ST</sub> of neutral loci to test if variation in a quantitative trait is a result of [[divergent selection]] or genetic drift, an analysis known as '''Q<sub>ST</sub>–F<sub>ST</sub> comparisons'''. |
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In [[quantitative genetics]], '''Q<sub>ST</sub>''' is a statistic intended to measure the degree of genetic differentiation among populations with regard to a [[quantitative trait]]. It was developed by Ken Spitze in 1993.<ref>{{Cite journal |last=Spitze |first=K. |date=October 1993 |title=Population structure in Daphnia obtusa: quantitative genetic and allozymic variation |journal=[[Genetics (journal)|Genetics]] |volume=135 |issue=2 |pages=367–374 |issn=0016-6731 |pmc=1205642 |pmid=8244001}}</ref> Its name reflects the fact that it was intended to be analogous to the [[fixation index]] for a single [[genetic locus]], which is denoted F<sub>ST</sub>.<ref>{{Cite journal |last=Whitlock |first=Michael C. |date=April 2008 |title=Evolutionary inference from QST |url=http://doi.wiley.com/10.1111/j.1365-294X.2008.03712.x |journal=[[Molecular Ecology]] |language=en |volume=17 |issue=8 |pages=1885–1896 |doi=10.1111/j.1365-294X.2008.03712.x}}</ref><ref>{{Cite journal |last=McKay |first=John K. |last2=Latta |first2=Robert G. |date=June 2002 |title=Adaptive population divergence: markers, QTL and traits |url=https://linkinghub.elsevier.com/retrieve/pii/S0169534702024783 |journal=[[Trends in Ecology & Evolution]] |language=en |volume=17 |issue=6 |pages=285–291 |doi=10.1016/S0169-5347(02)02478-3}}</ref> Q<sub>ST</sub> is often compared with F<sub>ST</sub> to test the hypothesis that a given quantitative trait has been the subject of [[divergent selection]] between the populations being studied. Generally, if Q<sub>ST</sub> is found to exceed F<sub>ST</sub>, this is interpreted as evidence of such divergent selection, because it indicates that there is more differentiation in the trait than could be produced solely by [[genetic drift]]. By contrast, if the values of Q<sub>ST</sub> and F<sub>ST</sub> in the same study are approximately equal, it is considered to reflect that the observed trait differentiation could be entirely due to genetic drift. However, the asssumptions on which these studies are based have been questioned.<ref>{{Cite journal |last=Pujol |first=B. |last2=Wilson |first2=A. J. |last3=Ross |first3=R. I. C. |last4=Pannell |first4=J. R. |date=November 2008|title=Are QST - FST comparisons for natural populations meaningful? |url=http://doi.wiley.com/10.1111/j.1365-294X.2008.03958.x |journal=Molecular Ecology |language=en |volume=17 |issue=22 |pages=4782–4785 |doi=10.1111/j.1365-294X.2008.03958.x}}</ref><ref>{{Cite journal |last=Leinonen |first=T. |last2=O’Hara |first2=R. B. |last3=Cano |first3=J. M. |last4=Merilä |first4=J. |date=January 2008 |title=Comparative studies of quantitative trait and neutral marker divergence: a meta-analysis |url=http://doi.wiley.com/10.1111/j.1420-9101.2007.01445.x |journal=[[Journal of Evolutionary Biology]] |language=en |volume=21 |issue=1 |pages=1–17 |doi=10.1111/j.1420-9101.2007.01445.x}}</ref><ref>{{Cite journal |last=Miller |first=Judith R. |last2=Wood |first2=Bryan P. |last3=Hamilton |first3=Matthew B. |date=October 2008 |title=FST and QST Under Neutrality |url=http://www.genetics.org/lookup/doi/10.1534/genetics.108.092031 |journal=Genetics |language=en |volume=180 |issue=2 |pages=1023–1037 |doi=10.1534/genetics.108.092031 |issn=0016-6731 |pmc=PMC2567353 |pmid=18780742}}</ref> |
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== Calculation of Q<sub>ST</sub> == |
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=== Equations === |
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{{Genetics-stub}} |
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Q<sub>ST</sub> represents the proportion of variance among subpopulations, and is it’s calculation is synonymous to F<sub>ST</sub> developed by [[Sewall Wright]].<ref>{{Cite journal | vauthors = Wright S |title=The Genetic Structure of Populations |url=https://doi.org/10.1111/j.1469-1809.1949.tb02451.x |journal=Annals of Eugenics |year=1949 |volume=15 |issue=4 |pages=323–354|doi=10.1111/j.1469-1809.1949.tb02451.x |pmid=24540312 }}</ref> However, instead of using genetic differentiation, Q<sub>ST</sub> is calculated by finding the variance of a quantitative trait within and among subpopulations, and for the total population.<ref name="Spitze_1993" /> Variance of a quantitative trait among populations (σ<sup>2</sup><sub>GB</sub>) is described as: |
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<math>\sigma_{GB}^2 = (1-Q_{ST})\sigma_T^2</math> |
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And the variance of a quantitative trait within populations (σ<sup>2</sup><sub>GW</sub>) is described as: |
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<math>\sigma _{GW}^2 = 2Q_{ST}\sigma_T^2</math> |
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Where σ<sup>2</sup><sub>T</sub> is the total genetic variance in all populations. Therefore, Q<sub>ST</sub> can be calculated with the following equation: |
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<math>Q_{ST} = \frac{\sigma_{GB}^2}{\sigma_{GB}^2 + 2\sigma_{GW}^2}</math> |
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=== Assumptions === |
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Calculation of Q<sub>ST</sub> is subject to several assumptions: populations must be in [[Hardy–Weinberg principle|Hardy-Weinberg Equilibrium]], observed variation is assumed to be due to [[additive genetic effects]] only, selection and [[linkage disequilibrium]] are not present,<ref name="Cubry_2017">{{cite journal | vauthors = Cubry P, Scotti I, Oddou-Muratorio S, Lefèvre F | title = Generalization of the Q<sub>ST</sub> framework in hierarchically structured populations: Impacts of inbreeding and dominance | journal = Molecular Ecology Resources | volume = 17 | issue = 6 | pages = e76–e83 | date = November 2017 | pmid = 28681534 | doi = 10.1111/1755-0998.12693 | s2cid = 206947951 | url = https://hal.archives-ouvertes.fr/hal-01576329/file/Cubry_etal_MainText_FinalDraft_2.pdf }}</ref> and the subpopulations exist within an island model.<ref name="de_Villemereuil_2022">{{Cite journal | vauthors = de Villemereuil P, Gaggiotti OE, Goudet J |date=2022 |title=Common garden experiments to study local adaptation need to account for population structure |journal=Journal of Ecology |volume=110 |issue=5 |pages=1005–1009 |doi=10.1111/1365-2745.13528 |s2cid=225136876 |issn=0022-0477|url=https://serval.unil.ch/notice/serval:BIB_07E8157C6B8F |hdl=10023/24327 |hdl-access=free }}</ref> |
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== Q<sub>ST</sub>-F<sub>ST</sub> comparisons == |
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Q<sub>ST</sub>–F<sub>ST</sub> analyses often involve culturing organisms in consistent environmental conditions, known as [[Transplant experiment|common garden experiments]],<ref name="Leinonen_2013">{{cite journal | vauthors = Leinonen T, McCairns RJ, O'Hara RB, Merilä J | title = Q(ST)-F(ST) comparisons: evolutionary and ecological insights from genomic heterogeneity | journal = Nature Reviews. Genetics | volume = 14 | issue = 3 | pages = 179–190 | date = March 2013 | pmid = 23381120 | doi = 10.1038/nrg3395 | s2cid = 6312222 }}</ref> and comparing the [[Phenotype|phenotypic]] variance to genetic variance. If Q<sub>ST</sub> is found to exceed F<sub>ST</sub>, this is interpreted as evidence of divergent selection, because it indicates more differentiation in the trait than could be produced solely by [[genetic drift]]. If Q<sub>ST</sub> is less than F<sub>ST</sub>, [[balancing selection]] is expected to be present. If the values of Q<sub>ST</sub> and F<sub>ST</sub>are equivalent, the observed trait differentiation could be due to genetic drift.<ref name="de_Villemereuil_2022" /> |
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Suitable comparison of Q<sub>ST</sub> and F<sub>ST</sub> is subject to multiple ecological and evolutionary assumptions,<ref>{{cite journal | vauthors = Pujol B, Wilson AJ, Ross RI, Pannell JR | title = Are Q(ST)-F(ST) comparisons for natural populations meaningful? | journal = Molecular Ecology | volume = 17 | issue = 22 | pages = 4782–4785 | date = November 2008 | pmid = 19140971 | doi = 10.1111/j.1365-294X.2008.03958.x | s2cid = 11707577 }}</ref><ref>{{cite journal | vauthors = Leinonen T, O'Hara RB, Cano JM, Merilä J | title = Comparative studies of quantitative trait and neutral marker divergence: a meta-analysis | journal = Journal of Evolutionary Biology | volume = 21 | issue = 1 | pages = 1–17 | date = January 2008 | pmid = 18028355 | doi = 10.1111/j.1420-9101.2007.01445.x | s2cid = 1037769 | doi-access = free }}</ref><ref>{{cite journal | vauthors = Miller JR, Wood BP, Hamilton MB | title = F(ST) and Q(ST) under neutrality | journal = Genetics | volume = 180 | issue = 2 | pages = 1023–1037 | date = October 2008 | pmid = 18780742 | pmc = 2567353 | doi = 10.1534/genetics.108.092031 }}</ref> and since the development of Q<sub>ST</sub>, multiple studies have examined the limitations and constrictions of Q<sub>ST</sub>-F<sub>ST</sub> analyses. Leinonen et al. notes F<sub>ST</sub> must be calculated with neutral loci, however over filtering of non-neutral loci can artificially reduce F<sub>ST</sub>values.<ref name="Leinonen_2013" /> Cubry et al. found Q<sub>ST</sub> is reduced in the presence of [[Dominance (genetics)|dominance]], resulting in conservative estimates of divergent selection when Q<sub>ST</sub> is high, and inconclusive results of balancing selection when Q<sub>ST</sub> is low.<ref name="Cubry_2017" /> Additionally, [[Population structure (genetics)|population structure]] can significantly impact Q<sub>ST</sub>-F<sub>ST</sub> ratios. Stepping stone models, which can generate more evolutionary noise than island models, are more likely to experience [[Type I and type II errors|type 1 errors]].<ref name="de_Villemereuil_2022" /> If a subset of populations act as sources, such as during [[Invasive species|invasion]], weighting the genetic contributions of each population can increase detection of adaptation.<ref name=":0">{{cite journal | vauthors = Marchini GL, Arredondo TM, Cruzan MB | title = Selective differentiation during the colonization and establishment of a newly invasive species | journal = Journal of Evolutionary Biology | volume = 31 | issue = 11 | pages = 1689–1703 | date = November 2018 | pmid = 30120791 | doi = 10.1111/jeb.13369 | s2cid = 52031406 | doi-access = free }}</ref> In order to improve precision of Q<sub>ST</sub> analyses, more populations (>20) should be included in analyses.<ref>{{cite journal | vauthors = O'Hara RB, Merilä J | title = Bias and precision in QST estimates: problems and some solutions | journal = Genetics | volume = 171 | issue = 3 | pages = 1331–1339 | date = November 2005 | pmid = 16085700 | pmc = 1456852 | doi = 10.1534/genetics.105.044545 }}</ref> |
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== Q<sub>ST</sub> applications in literature == |
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Multiple studies have incorporated Q<sub>ST</sub> to separate effects of [[natural selection]] and genetic drift, and Q<sub>ST</sub> is often observed to exceed F<sub>ST</sub>, indicating local adaptation.<ref>{{Cite journal |last1=Merilä |first1=J. |last2=Crnokrak |first2=P. |date=2001 |title=Comparison of genetic differentiation at marker loci and quantitative traits: Natural selection and genetic differentiation |url= |journal=Journal of Evolutionary Biology |language= |volume=14 |issue=6 |pages=892–903 |doi=10.1046/j.1420-9101.2001.00348.x|s2cid=83979407 |doi-access=free }}</ref> In an [[Restoration ecology|ecological restoration]] study, Bower and Aitken used Q<sub>ST</sub> to evaluate suitable populations for seed transfer of [[Pinus albicaulis|whitebark pine]]. They found high Q<sub>ST</sub> values in many populations, suggesting local adaptation for cold-adapted characteristics.<ref>{{Cite journal |last1=Bower |first1=Andrew D. |last2=Aitken |first2=Sally N. |date=2008 |title=Ecological genetics and seed transfer guidelines for Pinus albicaulis (Pinaceae) |url=http://doi.wiley.com/10.3732/ajb.95.1.66 |journal=American Journal of Botany |language=en |volume=95 |issue=1 |pages=66–76 |doi=10.3732/ajb.95.1.66|pmid=21632316 |doi-access=free }}</ref> During an assessment of the invasive species, ''[[Brachypodium sylvaticum]]'', Marchini et al. found divergence between native and invasive populations during initial establishment in the invaded range, but minimal divergence during [[Colonisation (biology)|range expansion]].<ref name=":0" /> In an examination of the common snapdragon (''[[Antirrhinum majus]]'') along an elevation gradient, Q<sub>ST</sub>-F<sub>ST</sub> analyses revealed different adaptation trends between two [[subspecies]] (''A. m. pseudomajus'' and ''A. m. striatum''). While both subspecies occur at all elevations, ''A. m. striatum'' had high Q<sub>ST</sub> values for traits associated with altitude adaptation: plant height, number of branches, and internode length. ''A. m. pseudomajus'' had lower Q<sub>ST</sub> than F<sub>ST</sub> values for germination time.<ref>{{Cite journal |last1=Marin |first1=Sara |last2=Gibert |first2=Anaïs |last3=Archambeau |first3=Juliette |last4=Bonhomme |first4=Vincent |last5=Lascoste |first5=Mylène |last6=Pujol |first6=Benoit |date=2020 |title=Potential adaptive divergence between subspecies and populations of snapdragon plants inferred from Q ST – F ST comparisons |journal=Molecular Ecology |language= |volume=29 |issue=16 |pages=3010–3021 |doi=10.1111/mec.15546 |issn=0962-1083 |pmc=7540467 |pmid=32652730}}</ref> |
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== See also == |
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* [[F-statistics]] |
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* [[Conservation genetics]] |
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* [[Divergent evolution|Divergent selection]] |
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* [[Genetic diversity]] |
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[[Category:Genetics terms]] |
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[[Category:Population genetics]] |
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[[Category:Statistical tests]] |
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Latest revision as of 01:42, 6 January 2024
In quantitative genetics, QST is a statistic intended to measure the degree of genetic differentiation among populations with regard to a quantitative trait. It was developed by Ken Spitze in 1993.[1] Its name reflects that QST was intended to be analogous to the fixation index for a single genetic locus (FST).[2][3] QST is often compared with FST of neutral loci to test if variation in a quantitative trait is a result of divergent selection or genetic drift, an analysis known as QST–FST comparisons.
Calculation of QST
[edit]Equations
[edit]QST represents the proportion of variance among subpopulations, and is it’s calculation is synonymous to FST developed by Sewall Wright.[4] However, instead of using genetic differentiation, QST is calculated by finding the variance of a quantitative trait within and among subpopulations, and for the total population.[1] Variance of a quantitative trait among populations (σ2GB) is described as:
And the variance of a quantitative trait within populations (σ2GW) is described as:
Where σ2T is the total genetic variance in all populations. Therefore, QST can be calculated with the following equation:
Assumptions
[edit]Calculation of QST is subject to several assumptions: populations must be in Hardy-Weinberg Equilibrium, observed variation is assumed to be due to additive genetic effects only, selection and linkage disequilibrium are not present,[5] and the subpopulations exist within an island model.[6]
QST-FST comparisons
[edit]QST–FST analyses often involve culturing organisms in consistent environmental conditions, known as common garden experiments,[7] and comparing the phenotypic variance to genetic variance. If QST is found to exceed FST, this is interpreted as evidence of divergent selection, because it indicates more differentiation in the trait than could be produced solely by genetic drift. If QST is less than FST, balancing selection is expected to be present. If the values of QST and FSTare equivalent, the observed trait differentiation could be due to genetic drift.[6]
Suitable comparison of QST and FST is subject to multiple ecological and evolutionary assumptions,[8][9][10] and since the development of QST, multiple studies have examined the limitations and constrictions of QST-FST analyses. Leinonen et al. notes FST must be calculated with neutral loci, however over filtering of non-neutral loci can artificially reduce FSTvalues.[7] Cubry et al. found QST is reduced in the presence of dominance, resulting in conservative estimates of divergent selection when QST is high, and inconclusive results of balancing selection when QST is low.[5] Additionally, population structure can significantly impact QST-FST ratios. Stepping stone models, which can generate more evolutionary noise than island models, are more likely to experience type 1 errors.[6] If a subset of populations act as sources, such as during invasion, weighting the genetic contributions of each population can increase detection of adaptation.[11] In order to improve precision of QST analyses, more populations (>20) should be included in analyses.[12]
QST applications in literature
[edit]Multiple studies have incorporated QST to separate effects of natural selection and genetic drift, and QST is often observed to exceed FST, indicating local adaptation.[13] In an ecological restoration study, Bower and Aitken used QST to evaluate suitable populations for seed transfer of whitebark pine. They found high QST values in many populations, suggesting local adaptation for cold-adapted characteristics.[14] During an assessment of the invasive species, Brachypodium sylvaticum, Marchini et al. found divergence between native and invasive populations during initial establishment in the invaded range, but minimal divergence during range expansion.[11] In an examination of the common snapdragon (Antirrhinum majus) along an elevation gradient, QST-FST analyses revealed different adaptation trends between two subspecies (A. m. pseudomajus and A. m. striatum). While both subspecies occur at all elevations, A. m. striatum had high QST values for traits associated with altitude adaptation: plant height, number of branches, and internode length. A. m. pseudomajus had lower QST than FST values for germination time.[15]
See also
[edit]References
[edit]- ^ a b Spitze K (October 1993). "Population structure in Daphnia obtusa: quantitative genetic and allozymic variation". Genetics. 135 (2): 367–374. doi:10.1093/genetics/135.2.367. PMC 1205642. PMID 8244001.
- ^ Whitlock MC (April 2008). "Evolutionary inference from QST". Molecular Ecology. 17 (8): 1885–1896. doi:10.1111/j.1365-294X.2008.03712.x. PMID 18363667.
- ^ McKay JK, Latta RG (June 2002). "Adaptive population divergence: markers, QTL and traits". Trends in Ecology & Evolution. 17 (6): 285–291. doi:10.1016/S0169-5347(02)02478-3.
- ^ Wright S (1949). "The Genetic Structure of Populations". Annals of Eugenics. 15 (4): 323–354. doi:10.1111/j.1469-1809.1949.tb02451.x. PMID 24540312.
- ^ a b Cubry P, Scotti I, Oddou-Muratorio S, Lefèvre F (November 2017). "Generalization of the QST framework in hierarchically structured populations: Impacts of inbreeding and dominance" (PDF). Molecular Ecology Resources. 17 (6): e76–e83. doi:10.1111/1755-0998.12693. PMID 28681534. S2CID 206947951.
- ^ a b c de Villemereuil P, Gaggiotti OE, Goudet J (2022). "Common garden experiments to study local adaptation need to account for population structure". Journal of Ecology. 110 (5): 1005–1009. doi:10.1111/1365-2745.13528. hdl:10023/24327. ISSN 0022-0477. S2CID 225136876.
- ^ a b Leinonen T, McCairns RJ, O'Hara RB, Merilä J (March 2013). "Q(ST)-F(ST) comparisons: evolutionary and ecological insights from genomic heterogeneity". Nature Reviews. Genetics. 14 (3): 179–190. doi:10.1038/nrg3395. PMID 23381120. S2CID 6312222.
- ^ Pujol B, Wilson AJ, Ross RI, Pannell JR (November 2008). "Are Q(ST)-F(ST) comparisons for natural populations meaningful?". Molecular Ecology. 17 (22): 4782–4785. doi:10.1111/j.1365-294X.2008.03958.x. PMID 19140971. S2CID 11707577.
- ^ Leinonen T, O'Hara RB, Cano JM, Merilä J (January 2008). "Comparative studies of quantitative trait and neutral marker divergence: a meta-analysis". Journal of Evolutionary Biology. 21 (1): 1–17. doi:10.1111/j.1420-9101.2007.01445.x. PMID 18028355. S2CID 1037769.
- ^ Miller JR, Wood BP, Hamilton MB (October 2008). "F(ST) and Q(ST) under neutrality". Genetics. 180 (2): 1023–1037. doi:10.1534/genetics.108.092031. PMC 2567353. PMID 18780742.
- ^ a b Marchini GL, Arredondo TM, Cruzan MB (November 2018). "Selective differentiation during the colonization and establishment of a newly invasive species". Journal of Evolutionary Biology. 31 (11): 1689–1703. doi:10.1111/jeb.13369. PMID 30120791. S2CID 52031406.
- ^ O'Hara RB, Merilä J (November 2005). "Bias and precision in QST estimates: problems and some solutions". Genetics. 171 (3): 1331–1339. doi:10.1534/genetics.105.044545. PMC 1456852. PMID 16085700.
- ^ Merilä, J.; Crnokrak, P. (2001). "Comparison of genetic differentiation at marker loci and quantitative traits: Natural selection and genetic differentiation". Journal of Evolutionary Biology. 14 (6): 892–903. doi:10.1046/j.1420-9101.2001.00348.x. S2CID 83979407.
- ^ Bower, Andrew D.; Aitken, Sally N. (2008). "Ecological genetics and seed transfer guidelines for Pinus albicaulis (Pinaceae)". American Journal of Botany. 95 (1): 66–76. doi:10.3732/ajb.95.1.66. PMID 21632316.
- ^ Marin, Sara; Gibert, Anaïs; Archambeau, Juliette; Bonhomme, Vincent; Lascoste, Mylène; Pujol, Benoit (2020). "Potential adaptive divergence between subspecies and populations of snapdragon plants inferred from Q ST – F ST comparisons". Molecular Ecology. 29 (16): 3010–3021. doi:10.1111/mec.15546. ISSN 0962-1083. PMC 7540467. PMID 32652730.